I see, I was not sure if you speak about annotations or scribles. I expected annotations to work in reflow, so came (wrongly) that you speak about scribles...
I do not use annotations, only scribles, so I do not know. Generaly, anotations should work in reflow and landscape. (From programmers side I might understand that there might be difficulties if reflow is used. But I do not see any reason in landscape and no reflow...)
There were/are problems with certain languages, or better said specific letters (with accents, etc.) in certain languages. And also for pdfs created from LaTex.
So, the cause of your problems might be language (or coding used) of pdf and not reflow/landscape setup of doc.